Package evaluation to test MendelIHT on Julia 1.14.0-DEV.2457 (6e8868916a*) started at 2026-06-29T00:45:32.506 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Activating project at `~/.julia/environments/v1.14` Set-up completed after 14.8s ################################################################################ # Installation # Installing MendelIHT... Resolving package versions... Updating `~/.julia/environments/v1.14/Project.toml` [921c7187] + MendelIHT v1.4.11 Updating `~/.julia/environments/v1.14/Manifest.toml` [7d9f7c33] + Accessors v0.1.45 [79e6a3ab] + Adapt v4.7.0 [66dad0bd] + AliasTables v1.1.3 [4fba245c] + ArrayInterface v7.27.0 [67c07d97] + Automa v1.2.0 ⌅ [6db4b851] + BGEN v0.1.17 [28d598bf] + BGZFStreams v0.3.2 [47718e42] + BioGenerics v0.1.5 [62783981] + BitTwiddlingConvenienceFunctions v0.1.6 [e1450e63] + BufferedStreams v1.2.2 [2a0fbf3d] + CPUSummary v0.2.7 [336ed68f] + CSV v0.10.16 [fb6a15b2] + CloseOpenIntervals v0.1.13 [523fee87] + CodecBzip2 v0.8.5 [ba30903b] + CodecXz v0.7.4 [944b1d66] + CodecZlib v0.7.8 [6b39b394] + CodecZstd v0.8.7 [861a8166] + Combinatorics v1.1.0 [38540f10] + CommonSolve v0.2.9 [f70d9fcc] + CommonWorldInvalidations v1.1.0 [34da2185] + Compat v4.18.1 [a33af91c] + CompositionsBase v0.1.2 [187b0558] + ConstructionBase v1.6.0 [adafc99b] + CpuId v0.3.1 [a8cc5b0e] + Crayons v4.1.1 [a10d1c49] + DBInterface v2.6.1 [9a962f9c] + 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[bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.2+0 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.15.0+0 [8e850ede] + nghttp2_jll v1.69.0+0 [3f19e933] + p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. To see why use `status --outdated -m` Installation completed after 5.89s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompiling project... 5.0 s ✓ BGEN 8.3 s ✓ VCFTools 28.6 s ✓ SnpArrays WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import.  NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions.  NOTE: This behavior may have differed in Julia versions prior to 1.12.  Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`.  Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. 26.5 s ✓ MendelIHT 4 dependencies successfully precompiled in 75 seconds. 171 already precompiled. 1 dependency had output during precompilation: ┌ MendelIHT │ WARNING: Constructor for type "MvNormal" was extended in `MendelIHT` without explicit qualification or import. │ NOTE: Assumed "MvNormal" refers to `Distributions.MvNormal`. This behavior is deprecated and may differ in future versions. │ NOTE: This behavior may have differed in Julia versions prior to 1.12. │ Hint: If you intended to create a new generic function of the same name, use `function MvNormal end`. │ Hint: To silence the warning, qualify `MvNormal` as `Distributions.MvNormal` in the method signature or explicitly `import Distributions: MvNormal`. └ Precompilation completed after 99.66s ################################################################################ # Testing # Testing MendelIHT Status `/tmp/jl_hmvX4C/Project.toml` ⌅ [6db4b851] BGEN v0.1.17 [6e4b80f9] BenchmarkTools v1.8.0 [336ed68f] CSV v0.10.16 [a93c6f00] DataFrames v1.8.2 [8bb1440f] DelimitedFiles v1.9.1 [b4f34e82] Distances v0.10.12 [31c24e10] Distributions v0.25.129 [38e38edf] GLM v1.9.5 [921c7187] MendelIHT v1.4.11 [92933f4c] ProgressMeter v1.11.0 [189a3867] Reexport v1.2.2 [4e780e97] SnpArrays v0.3.23 [276daf66] SpecialFunctions v2.8.0 [2913bbd2] StatsBase v0.34.12 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nghttp2_jll v1.69.0+0 [3f19e933] p7zip_jll v17.8.0+0 Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading. Testing Running tests... ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = Distributions.MvNormal(σ::Vector{Float64}) at mvnormal.jl:207 └ @ Distributions ~/.julia/packages/Distributions/XAng5/src/multivariate/mvnormal.jl:207 ┌ Warning: `MvNormal(σ::AbstractVector{<:Real})` is deprecated, use `MvNormal(LinearAlgebra.Diagonal(map(abs2, σ)))` instead. │ caller = ip:0x0 └ @ Core :-1 ┌ Warning: `cholesky!(A::RealHermSymComplexHerm{<:Real}, ::Val{true}; kwargs...)` is deprecated, use `cholesky!(A, RowMaximum(); kwargs...)` instead. │ caller = iht_stepsize!(v::MendelIHT.mIHTVariable{Float64, LinearAlgebra.Transpose{Float64, SnpArrays.SnpLinAlg{Float64}}}) at multivariate.jl:241 └ @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/multivariate.jl:241 Test Summary: | Pass Total Time loglikelihood | 4 4 15.9s Test Summary: | Pass Total Time deviance | 1 1 0.4s Test Summary: | Pass Total Time update_μ! | 4 4 1.6s Test Summary: | Pass Total Time _choose! | 7 7 9.9s Test Summary: | Pass Total Time _iht_backtrack | 7 7 0.0s Test Summary: | Pass Total Time standardize! | 12 12 1.3s Test Summary: | Pass Total Time project_k! | 2 2 1.1s Test Summary: | Pass Total Time project_group_sparse! | 5 5 1.1s Test Summary: | Pass Total Time maf_weights | 6 6 2.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1691.574564060963, backtracks = 0, tol = 1.7839624301381212 Iteration 2: loglikelihood = -1426.432636469604, backtracks = 0, tol = 0.16600329573789366 Iteration 3: loglikelihood = -1393.949902759375, backtracks = 0, tol = 0.05798306479580661 Iteration 4: loglikelihood = -1392.9204594815913, backtracks = 0, tol = 0.00959293446644763 Iteration 5: loglikelihood = -1392.6952323000219, backtracks = 0, tol = 0.03431453529526753 Iteration 6: loglikelihood = -1392.648727292017, backtracks = 1, tol = 0.001421116244599894 Iteration 7: loglikelihood = -1392.6369078954863, backtracks = 1, tol = 0.0007231670434762891 Iteration 8: loglikelihood = -1392.6339131262826, backtracks = 1, tol = 0.0003653853814443613 Iteration 9: loglikelihood = -1392.6331564598222, backtracks = 1, tol = 0.0001836037200475528 Iteration 10: loglikelihood = -1392.6329657376782, backtracks = 1, tol = 9.190684927633979e-5 IHT estimated 10 nonzero SNP predictors and 1 non-genetic predictors. Compute time (sec): 0.09233498573303223 Final loglikelihood: -1392.6329657376782 SNP PVE: 0.9346232496390215 Iterations: 10 Selected genetic predictors: 10×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 157 0.473759 2 │ 367 1.99533 3 │ 712 -0.107801 4 │ 1380 1.06027 5 │ 3639 1.14641 6 │ 4181 -0.487325 7 │ 5517 2.15523 8 │ 7323 1.1499 9 │ 7663 -0.121264 10 │ 9895 -1.04874 Selected nongenetic predictors: 1×2 DataFrame Row │ Position Estimated_β │ Int64 Float64 ─────┼─────────────────────── 1 │ 1 -0.03932Test Summary: | Pass Total Time fit normal SnpLinAlg | 4 4 23.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse logistic regression Number of threads = 1 Link functin = LogitLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -379.72375963518977, backtracks = 0, tol = 0.6062552017348442 Iteration 2: loglikelihood = -294.14222098196217, backtracks = 0, tol = 0.39035964909167 Iteration 3: loglikelihood = -258.44215825745147, backtracks = 0, tol = 0.18072720194601524 Iteration 4: loglikelihood = -248.39092317275637, backtracks = 1, tol = 0.0581811999889429 Iteration 5: loglikelihood = -241.2861695402178, backtracks = 2, tol = 0.10199490430383734 Iteration 6: loglikelihood = -236.0344401262056, backtracks = 2, tol = 0.10444957184614982 Iteration 7: loglikelihood = -232.75639772007577, backtracks = 2, tol = 0.03618239958756675 Iteration 8: loglikelihood = -230.9028935826695, backtracks = 3, tol = 0.022566251649321353 Iteration 9: loglikelihood = -229.2332883500926, backtracks = 3, tol = 0.02394599965909332 Iteration 10: loglikelihood = -227.8109863155336, backtracks = 3, tol = 0.02260237147851236 Iteration 11: loglikelihood = -226.61429831284372, backtracks = 3, tol = 0.02153016573221634 Iteration 12: loglikelihood = -225.614543213995, backtracks = 3, tol = 0.020073248773013197 Iteration 13: loglikelihood = -225.15228734295533, backtracks = 3, tol = 0.10266272165892033 Iteration 14: loglikelihood = -224.5524858306654, backtracks = 2, tol = 0.010910053499902256 Iteration 15: loglikelihood = -223.90430308527087, backtracks = 3, tol = 0.10669566586572145 Iteration 16: loglikelihood = -223.43342440058004, backtracks = 1, tol = 0.009912340440473734 Iteration 17: loglikelihood = -223.19474883510568, backtracks = 3, tol = 0.10429355504005154 Iteration 18: loglikelihood = -222.7530868660152, backtracks = 1, tol = 0.010133510239484585 Iteration 19: loglikelihood = -222.4546375562022, backtracks = 3, tol = 0.009382230171462355 Iteration 20: loglikelihood = -225.04961416047087, backtracks = 3, tol = 0.13141028198780508 Iteration 21: loglikelihood = -221.57583298738808, backtracks = 0, tol = 0.12983606150115481 Iteration 22: loglikelihood = -220.9953587123894, backtracks = 0, tol = 0.018278220962270587 Iteration 23: loglikelihood = -220.46528702030645, backtracks = 0, tol = 0.10912949798131547 Iteration 24: loglikelihood = -220.22939682199817, backtracks = 1, tol = 0.006133557493960293 Iteration 25: loglikelihood = -220.1149031779291, backtracks = 3, tol = 0.005637364497494655 Iteration 26: loglikelihood = -237.91408320706802, backtracks = 3, tol = 0.1311916630585333 Iteration 27: loglikelihood = -222.6667401701631, backtracks = 0, tol = 0.13008576394077564 Iteration 28: loglikelihood = -220.0179912284672, backtracks = 0, tol = 0.10981267805412102 Iteration 29: loglikelihood = -219.80873468505163, backtracks = 1, tol = 0.006242686572879014 Iteration 30: loglikelihood = -219.71412932030552, backtracks = 1, tol = 0.0052581541847830735 Iteration 31: loglikelihood = -219.67346582214395, backtracks = 3, tol = 0.002736072071808146 Iteration 32: loglikelihood = -236.63118723570068, backtracks = 3, tol = 0.12536959025201838 Iteration 33: loglikelihood = -222.42522446507616, backtracks = 0, tol = 0.12480632457239557 Iteration 34: loglikelihood = -219.76952387571325, backtracks = 0, tol = 0.10782393864869841 Iteration 35: loglikelihood = -219.54239052596037, backtracks = 0, tol = 0.010969385336776636 Iteration 36: loglikelihood = -219.51051719556185, backtracks = 0, tol = 0.0038143069815270263 Iteration 37: loglikelihood = -219.49562270628724, backtracks = 1, tol = 0.0015360028505860806 Iteration 38: loglikelihood = -222.2776344615594, backtracks = 3, tol = 0.10706948875570901 Iteration 39: loglikelihood = -219.86344247649652, backtracks = 0, tol = 0.10682440099239575 Iteration 40: loglikelihood = -219.50637292175287, backtracks = 0, tol = 0.010145149683589566 Iteration 41: loglikelihood = -219.45601478260392, backtracks = 0, tol = 0.004786594360325445 Iteration 42: loglikelihood = -219.44279315931445, backtracks = 0, tol = 0.0023300326568676676 Iteration 43: loglikelihood = -219.434262597912, backtracks = 0, tol = 0.002159682320412748 Iteration 44: loglikelihood = -219.42706752504972, backtracks = 0, tol = 0.0019986878272562235 Iteration 45: loglikelihood = -219.4208881668612, backtracks = 0, tol = 0.001781315196828412 Iteration 46: loglikelihood = -219.41556755717227, backtracks = 0, tol = 0.0017266268818688624 Iteration 47: loglikelihood = -219.41098445944962, backtracks = 0, tol = 0.001504993867218278 Iteration 48: loglikelihood = -219.4070309112888, backtracks = 0, tol = 0.001495426527055874 Iteration 49: loglikelihood = -219.40362030781677, backtracks = 0, tol = 0.001286324051089446 Iteration 50: loglikelihood = -219.4006747755802, backtracks = 0, tol = 0.001295957349435961 Iteration 51: loglikelihood = -219.39813103252988, backtracks = 0, tol = 0.0011058748112207813 Iteration 52: loglikelihood = -219.3959322024177, backtracks = 0, tol = 0.0011233728145861855 Iteration 53: loglikelihood = -219.39403166729804, backtracks = 0, tol = 0.0009536994758608786 Iteration 54: loglikelihood = -219.39238763268273, backtracks = 0, tol = 0.0009739180646352119 Iteration 55: loglikelihood = -219.39096560226784, backtracks = 0, tol = 0.0008239389039648708 Iteration 56: loglikelihood = -219.38973473800374, backtracks = 0, tol = 0.0008444580901064712 Iteration 57: loglikelihood = -219.3886694316569, backtracks = 0, tol = 0.0007126409505425607 Iteration 58: loglikelihood = -219.38774685610232, backtracks = 0, tol = 0.0007323063866727435 Iteration 59: loglikelihood = -219.3869479529937, backtracks = 0, tol = 0.00061686194275372 Iteration 60: loglikelihood = -219.3862557798823, backtracks = 0, tol = 0.0006351404346176769 Iteration 61: loglikelihood = -219.3856561234815, backtracks = 0, tol = 0.000534269842115572 Iteration 62: loglikelihood = -219.38513638040487, backtracks = 0, tol = 0.0005509480422217535 Iteration 63: loglikelihood = -219.38468593224545, backtracks = 0, tol = 0.0004629512780606966 Iteration 64: loglikelihood = -219.38429538513583, backtracks = 0, tol = 0.0004779860767529819 Iteration 65: loglikelihood = -219.38395679466737, backtracks = 0, tol = 0.0004013057505476397 Iteration 66: loglikelihood = -219.38366314739872, backtracks = 0, tol = 0.0004147454994836376 Iteration 67: loglikelihood = -219.38340849212824, backtracks = 0, tol = 0.00034797985178746597 Iteration 68: loglikelihood = -219.38318758502183, backtracks = 0, tol = 0.0003599207374415984 Iteration 69: loglikelihood = -219.38299596326374, backtracks = 0, tol = 0.0003018217223394219 Iteration 70: loglikelihood = -219.3828297011887, backtracks = 0, tol = 0.00031238270039476616 Iteration 71: loglikelihood = -219.38268544908368, backtracks = 0, tol = 0.00026184698528793125 Iteration 72: loglikelihood = -219.3825602648841, backtracks = 0, tol = 0.0002711550905775348 Iteration 73: loglikelihood = -219.38245163239276, backtracks = 0, tol = 0.00022721198022395564 Iteration 74: loglikelihood = -219.38235734460943, backtracks = 0, tol = 0.00023539371282360467 Iteration 75: loglikelihood = -219.38227551018164, backtracks = 0, tol = 0.0001971920991460162 Iteration 76: loglikelihood = -219.382204472153, backtracks = 0, tol = 0.00020436848993624394 Iteration 77: loglikelihood = -219.3821428080304, backtracks = 0, tol = 0.00017116393516432852 Iteration 78: loglikelihood = -219.38208927292968, backtracks = 0, tol = 0.00017744788492952903 Iteration 79: loglikelihood = -219.38204279645043, backtracks = 0, tol = 0.00014859040670150365 Iteration 80: loglikelihood = -219.38200244272016, backtracks = 0, tol = 0.00015408544066832546 Iteration 81: loglikelihood = -219.38196740593906, backtracks = 0, tol = 0.00012900826739905896 Iteration 82: loglikelihood = -219.38193698216227, backtracks = 0, tol = 0.00013380816660865064 Iteration 83: loglikelihood = -219.38191056455443, backtracks = 0, tol = 0.00011201756190578927 Iteration 84: loglikelihood = -219.3818876233726, backtracks = 0, tol = 0.000116206527337935 Iteration 85: loglikelihood = -219.38186770147453, backtracks = 0, tol = 9.727268703830643e-5 Test Summary: | Pass Total Time fit Bernoulli SnpLinAlg | 4 4 3.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Poisson regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2197.7721687926255, backtracks = 0, tol = 0.3247876031204139 Iteration 2: loglikelihood = -1567.0334121333935, backtracks = 0, tol = 0.06231267372328574 Iteration 3: loglikelihood = -1447.7756085872818, backtracks = 0, tol = 0.05632622299962031 Iteration 4: loglikelihood = -1395.4281930335592, backtracks = 0, tol = 0.10597798312382947 Iteration 5: loglikelihood = -1369.2425006329297, backtracks = 0, tol = 0.05670682742115082 Iteration 6: loglikelihood = -1356.9427578681282, backtracks = 0, tol = 0.03515391752662177 Iteration 7: loglikelihood = -1350.6321755655424, backtracks = 1, tol = 0.021181717863022854 Iteration 8: loglikelihood = -1347.5976874535575, backtracks = 1, tol = 0.020028417652569096 Iteration 9: loglikelihood = -1345.1538462274455, backtracks = 1, tol = 0.014175870211404734 Iteration 10: loglikelihood = -1344.156203437423, backtracks = 1, tol = 0.010520059822768749 Iteration 11: loglikelihood = -1343.5105841940226, backtracks = 2, tol = 0.005765187641326613 Iteration 12: loglikelihood = -1342.9169991876047, backtracks = 2, tol = 0.00833065794796181 Iteration 13: loglikelihood = -1342.5655972535537, backtracks = 2, tol = 0.005415590136500304 Iteration 14: loglikelihood = -1342.3514665257776, backtracks = 2, tol = 0.004903092259453015 Iteration 15: loglikelihood = -1342.2164638306022, backtracks = 2, tol = 0.0032412186918024813 Iteration 16: loglikelihood = -1342.1307585365478, backtracks = 2, tol = 0.0030857807438150575 Iteration 17: loglikelihood = -1342.075828135697, backtracks = 2, tol = 0.002050371469158632 Iteration 18: loglikelihood = -1342.0406588372148, backtracks = 2, tol = 0.0019734999397025684 Iteration 19: loglikelihood = -1342.0180186440393, backtracks = 2, tol = 0.0013104528722270392 Iteration 20: loglikelihood = -1342.0034593528756, backtracks = 2, tol = 0.001268548153421455 Iteration 21: loglikelihood = -1341.9940632793277, backtracks = 2, tol = 0.0008418731683286065 Iteration 22: loglikelihood = -1341.9880042039397, backtracks = 2, tol = 0.0008178615301040556 Iteration 23: loglikelihood = -1341.9840878904338, backtracks = 2, tol = 0.0005425603170168813 Iteration 24: loglikelihood = -1341.9815579885758, backtracks = 2, tol = 0.0005282799994113808 Iteration 25: loglikelihood = -1341.9799212108119, backtracks = 2, tol = 0.0003503613385899931 Iteration 26: loglikelihood = -1341.9788626676348, backtracks = 2, tol = 0.0003416347150458818 Iteration 27: loglikelihood = -1341.9781774049056, backtracks = 2, tol = 0.0002265356509901648 Iteration 28: loglikelihood = -1341.977733904767, backtracks = 2, tol = 0.00022109939940117638 Iteration 29: loglikelihood = -1341.9774466880115, backtracks = 2, tol = 0.0001465922634598301 Iteration 30: loglikelihood = -1341.9772607141963, backtracks = 2, tol = 0.0001431605908180985 Iteration 31: loglikelihood = -1341.977140245208, backtracks = 2, tol = 9.4910332589348e-5 Test Summary: | Pass Total Time fit Poisson SnpLinAlg | 4 4 3.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1590.2399072704995, backtracks = 0, tol = 0.30873377934359325 Iteration 2: loglikelihood = -1514.0488490557916, backtracks = 0, tol = 0.18772071004699575 Iteration 3: loglikelihood = -1492.7804309656133, backtracks = 0, tol = 0.13100806638760842 Iteration 4: loglikelihood = -1489.1228692363482, backtracks = 0, tol = 0.07967862138811069 Iteration 5: loglikelihood = -1487.6480040292693, backtracks = 0, tol = 0.06679085175938715 Iteration 6: loglikelihood = -1487.1557669284125, backtracks = 0, tol = 0.06579972219240646 Iteration 7: loglikelihood = -1486.2402879743292, backtracks = 0, tol = 0.06032710460631914 Iteration 8: loglikelihood = -1485.5501409168714, backtracks = 0, tol = 0.0651762325057049 Iteration 9: loglikelihood = -1485.4580586950085, backtracks = 0, tol = 0.006291254685750656 Iteration 10: loglikelihood = -1485.451021335357, backtracks = 0, tol = 0.0017868439888444265 Iteration 11: loglikelihood = -1485.4501421045268, backtracks = 1, tol = 0.0005298915029214036 Iteration 12: loglikelihood = -1485.4497274894784, backtracks = 1, tol = 0.00040744447733770547 Iteration 13: loglikelihood = -1485.4495950104865, backtracks = 1, tol = 0.00019340503440719786 Iteration 14: loglikelihood = -1485.4495571663394, backtracks = 1, tol = 0.00012206932079446037 Iteration 15: loglikelihood = -1485.4495471497034, backtracks = 1, tol = 5.7611076761376004e-5 Test Summary: | Pass Total Time fit NegativeBinomial SnpLinAlg | 4 4 1.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1986.5457178958602, backtracks = 0, tol = 0.7403647707185224 Iteration 2: loglikelihood = -1528.7945819245508, backtracks = 0, tol = 0.1508121855909614 Iteration 3: loglikelihood = -1407.9575215200923, backtracks = 0, tol = 0.06387983308652596 Iteration 4: loglikelihood = -1394.423743828546, backtracks = 0, tol = 0.02878704335307475 Iteration 5: loglikelihood = -1391.5423958060421, backtracks = 0, tol = 0.026294799057169103 Iteration 6: loglikelihood = -1391.4091877932392, backtracks = 0, tol = 0.02407660136567296 Iteration 7: loglikelihood = -1389.7900148482747, backtracks = 0, tol = 0.023807901671242204 Iteration 8: loglikelihood = -1389.6220232821763, backtracks = 1, tol = 0.0014503636786846272 Iteration 9: loglikelihood = -1389.5791891553104, backtracks = 1, tol = 0.0007797339421318618 Iteration 10: loglikelihood = -1389.5683208010523, backtracks = 1, tol = 0.00041010594125970876 Iteration 11: loglikelihood = -1389.565573432758, backtracks = 1, tol = 0.00021217643951493024 Iteration 12: loglikelihood = -1389.564880799794, backtracks = 1, tol = 0.00010846595290002274 Iteration 13: loglikelihood = -1389.5647065080345, backtracks = 1, tol = 5.497456336756304e-5 Test Summary: | Pass Total Time fit with >1 non-genetic covariates SnpLinAlg | 5 5 1.7s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1644.020576800052, backtracks = 0, tol = 0.5353661813227376 Iteration 2: loglikelihood = -1425.7402064749092, backtracks = 0, tol = 0.09591811192661069 Iteration 3: loglikelihood = -1402.8458090577162, backtracks = 0, tol = 0.048864381048990845 Iteration 4: loglikelihood = -1390.891967858794, backtracks = 0, tol = 0.0327157344798591 Iteration 5: loglikelihood = -1389.2991733964234, backtracks = 0, tol = 0.028212439100665777 Iteration 6: loglikelihood = -1389.1475927934368, backtracks = 1, tol = 0.0014777006298075845 Iteration 7: loglikelihood = -1389.1082104662376, backtracks = 1, tol = 0.0007966337556314169 Iteration 8: loglikelihood = -1389.0979956212132, backtracks = 1, tol = 0.0004247226875400627 Iteration 9: loglikelihood = -1389.095358883154, backtracks = 1, tol = 0.00022328937382627058 Iteration 10: loglikelihood = -1389.0946828591473, backtracks = 1, tol = 0.00011572984833979894 Iteration 11: loglikelihood = -1389.094510738556, backtracks = 1, tol = 5.9259531912212026e-5 Test Summary: | Pass Total Time model selection on non-genetic covariates | 5 5 0.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 15 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1473.12410014528, backtracks = 0, tol = 0.11162633196865429 Iteration 2: loglikelihood = -1448.37403799896, backtracks = 0, tol = 0.07736217654955346 Iteration 3: loglikelihood = -1429.8981769610311, backtracks = 1, tol = 0.056531823476744666 Iteration 4: loglikelihood = -1404.7133956159753, backtracks = 0, tol = 0.10125409614175711 Iteration 5: loglikelihood = -1397.466171579031, backtracks = 0, tol = 0.05343369325195712 Iteration 6: loglikelihood = -1395.7490747391416, backtracks = 0, tol = 0.08843871418165569 Iteration 7: loglikelihood = -1395.4877576477586, backtracks = 0, tol = 0.0089247040684952 Iteration 8: loglikelihood = -1395.442237061722, backtracks = 0, tol = 0.005277867116132827 Iteration 9: loglikelihood = -1395.4302205892106, backtracks = 0, tol = 0.0027680467744013336 Iteration 10: loglikelihood = -1395.1973617039414, backtracks = 0, tol = 0.0905690065560604 Iteration 11: loglikelihood = -1395.0048067729406, backtracks = 0, tol = 0.007650485819168939 Iteration 12: loglikelihood = -1394.9835209063683, backtracks = 0, tol = 0.0035232591741737973 Iteration 13: loglikelihood = -1394.9793628241396, backtracks = 0, tol = 0.001852195878065177 Iteration 14: loglikelihood = -1394.9779889816232, backtracks = 0, tol = 0.0012530451800711444 Iteration 15: loglikelihood = -1394.977503420045, backtracks = 0, tol = 0.0006829444661300923 Iteration 16: loglikelihood = -1394.9773714862843, backtracks = 1, tol = 0.00022881022816864142 Iteration 17: loglikelihood = -1394.977310220191, backtracks = 2, tol = 0.0001217788197399568 Iteration 18: loglikelihood = -1394.977273607278, backtracks = 2, tol = 8.822469907087602e-5 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 3 Prior weight scaling = off Doubly sparse projection = on Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1535.4672180567934, backtracks = 0, tol = 0.17016419679985048 Iteration 2: loglikelihood = -1508.04343741211, backtracks = 0, tol = 0.21718489399873087 Iteration 3: loglikelihood = -1448.2717322168082, backtracks = 0, tol = 0.15334504607402907 Iteration 4: loglikelihood = -1437.5669418734744, backtracks = 0, tol = 0.08425396177776269 Iteration 5: loglikelihood = -1434.3602241747528, backtracks = 0, tol = 0.03199716666887782 Iteration 6: loglikelihood = -1434.239273652971, backtracks = 2, tol = 0.003498168340088273 Iteration 7: loglikelihood = -1434.1475478538455, backtracks = 2, tol = 0.0030522911015526556 Iteration 8: loglikelihood = -1434.0913475157126, backtracks = 2, tol = 0.0021931576818355514 Iteration 9: loglikelihood = -1434.0584761985995, backtracks = 2, tol = 0.0016688209654910561 Iteration 10: loglikelihood = -1434.0393127719108, backtracks = 2, tol = 0.001317554485128468 Iteration 11: loglikelihood = -1434.0281644425422, backtracks = 2, tol = 0.0010393713220469248 Iteration 12: loglikelihood = -1434.0216963632631, backtracks = 2, tol = 0.0008158673348111212 Iteration 13: loglikelihood = -1434.0179556115852, backtracks = 2, tol = 0.0006363671566384319 Iteration 14: loglikelihood = -1433.8972844529703, backtracks = 2, tol = 0.02105646084267335 Iteration 15: loglikelihood = -1433.6170929347984, backtracks = 1, tol = 0.011448126839540936 Iteration 16: loglikelihood = -1433.5408744767515, backtracks = 2, tol = 0.0040324300639331045 Iteration 17: loglikelihood = -1433.4945867179188, backtracks = 2, tol = 0.003005268578298657 Iteration 18: loglikelihood = -1433.467626121943, backtracks = 2, tol = 0.002187229771831438 Iteration 19: loglikelihood = -1433.4521439235273, backtracks = 2, tol = 0.0016467936133078437 Iteration 20: loglikelihood = -1433.4432822302874, backtracks = 2, tol = 0.0012631945762950846 Iteration 21: loglikelihood = -1433.4382075829426, backtracks = 2, tol = 0.0009580287583338291 Iteration 22: loglikelihood = -1433.4352962137846, backtracks = 2, tol = 0.0007222437442123496 Iteration 23: loglikelihood = -1433.4336216439426, backtracks = 2, tol = 0.0005424739396431532 Iteration 24: loglikelihood = -1433.43265547142, backtracks = 2, tol = 0.00040628145880685523 Iteration 25: loglikelihood = -1433.4320960523787, backtracks = 2, tol = 0.0003034179918772475 Iteration 26: loglikelihood = -1433.4317709097872, backtracks = 2, tol = 0.00022583740291084404 Iteration 27: loglikelihood = -1433.4315812027676, backtracks = 2, tol = 0.0001673653861249394 Iteration 28: loglikelihood = -1432.5898379532837, backtracks = 2, tol = 0.025080215054031605 Iteration 29: loglikelihood = -1431.7678006470733, backtracks = 1, tol = 0.017181190475547538 Iteration 30: loglikelihood = -1430.3157393955933, backtracks = 1, tol = 0.07333968264200234 Iteration 31: loglikelihood = -1429.706868513855, backtracks = 0, tol = 0.020015111727945754 Iteration 32: loglikelihood = -1429.5802551945537, backtracks = 1, tol = 0.00756937670420323 Iteration 33: loglikelihood = -1429.5139450553559, backtracks = 2, tol = 0.003906515984506227 Iteration 34: loglikelihood = -1429.4691972325213, backtracks = 2, tol = 0.003683664863256486 Iteration 35: loglikelihood = -1428.8607526222902, backtracks = 2, tol = 0.08711763846658777 Iteration 36: loglikelihood = -1428.6178427111051, backtracks = 1, tol = 0.006558345246943271 Iteration 37: loglikelihood = -1428.5424083746184, backtracks = 2, tol = 0.0033912200662443866 Iteration 38: loglikelihood = -1428.4933608487952, backtracks = 2, tol = 0.0030098214824111793 Iteration 39: loglikelihood = -1428.4620745885088, backtracks = 2, tol = 0.0025951371119133128 Iteration 40: loglikelihood = -1428.4427329028306, backtracks = 2, tol = 0.002148184701148465 Iteration 41: loglikelihood = -1428.4311433050725, backtracks = 2, tol = 0.0017160493175770867 Iteration 42: loglikelihood = -1428.4243474878394, backtracks = 2, tol = 0.0013407892924840973 Iteration 43: loglikelihood = -1428.420413936832, backtracks = 2, tol = 0.0010343694042998534 Iteration 44: loglikelihood = -1428.4181556141762, backtracks = 2, tol = 0.0007948565534422845 Iteration 45: loglikelihood = -1428.4168664091337, backtracks = 2, tol = 0.000608309643427293 Iteration 46: loglikelihood = -1428.4161334920516, backtracks = 2, tol = 0.0004622621654004415 Iteration 47: loglikelihood = -1428.4157180925672, backtracks = 2, tol = 0.00034956951660978575 Iteration 48: loglikelihood = -1428.4154831711999, backtracks = 2, tol = 0.00026348047442121094 Iteration 49: loglikelihood = -1428.4153505233908, backtracks = 2, tol = 0.00019816133989405092 Iteration 50: loglikelihood = -1428.4152757065372, backtracks = 2, tol = 0.00014882628973647444 Iteration 51: loglikelihood = -1428.4152335404317, backtracks = 2, tol = 0.00011167501044822909 Iteration 52: loglikelihood = -1428.4152097888611, backtracks = 2, tol = 8.375238803842589e-5 Test Summary: | Pass Total Time Correlated predictors and double sparsity Float64 matrix | 2 2 10.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1448.1093711026274, backtracks = 0, tol = 0.20870573796757916 Iteration 2: loglikelihood = -1413.0332759217185, backtracks = 0, tol = 0.10442266621333716 Iteration 3: loglikelihood = -1381.4979395921393, backtracks = 0, tol = 0.10145931801416798 Iteration 4: loglikelihood = -1371.0361304691148, backtracks = 0, tol = 0.08620160226258353 Iteration 5: loglikelihood = -1353.6265456476217, backtracks = 0, tol = 0.05594632142767635 Iteration 6: loglikelihood = -1341.4903643757298, backtracks = 0, tol = 0.06715726165074372 Iteration 7: loglikelihood = -1336.849341870308, backtracks = 0, tol = 0.03766847819114209 Iteration 8: loglikelihood = -1335.6151217021434, backtracks = 0, tol = 0.024569829998813162 Iteration 9: loglikelihood = -1333.55843528562, backtracks = 0, tol = 0.06528191257398576 Iteration 10: loglikelihood = -1333.2494232399038, backtracks = 1, tol = 0.006668980656214161 Iteration 11: loglikelihood = -1333.1121221060414, backtracks = 1, tol = 0.004537156817144087 Iteration 12: loglikelihood = -1333.083690134087, backtracks = 2, tol = 0.0021038053148142804 Iteration 13: loglikelihood = -1333.0659682441635, backtracks = 2, tol = 0.0016042052966634768 Iteration 14: loglikelihood = -1333.0558202342127, backtracks = 2, tol = 0.0012370314140366981 Iteration 15: loglikelihood = -1333.0500552306207, backtracks = 2, tol = 0.0009435314075004901 Iteration 16: loglikelihood = -1333.0467945777968, backtracks = 2, tol = 0.0007147987620433379 Iteration 17: loglikelihood = -1333.0449548598008, backtracks = 2, tol = 0.0005394407330376906 Iteration 18: loglikelihood = -1333.043918287385, backtracks = 2, tol = 0.00040617612028338005 Iteration 19: loglikelihood = -1333.0433347110632, backtracks = 2, tol = 0.0003054070001713478 Iteration 20: loglikelihood = -1333.0430063269155, backtracks = 2, tol = 0.00022943406973105322 Iteration 21: loglikelihood = -1333.0428215994868, backtracks = 2, tol = 0.00017225944523675794 Iteration 22: loglikelihood = -1333.0427177052118, backtracks = 2, tol = 0.00012928147669868766 Iteration 23: loglikelihood = -1333.0426592811757, backtracks = 2, tol = 9.699970253242232e-5 1.284053 seconds (5.51 M allocations: 96.637 MiB, 1.99% gc time, 48.82% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -1484.530770322406, backtracks = 0, tol = 0.20870573796757916 Iteration 2: loglikelihood = -1452.8197657014553, backtracks = 0, tol = 0.12624389879905132 Iteration 3: loglikelihood = -1436.1813331189742, backtracks = 0, tol = 0.10084418581182421 Iteration 4: loglikelihood = -1418.3231452644472, backtracks = 0, tol = 0.0834361270014998 Iteration 5: loglikelihood = -1404.4471453001731, backtracks = 0, tol = 0.06510889766381664 Iteration 6: loglikelihood = -1391.038482698739, backtracks = 0, tol = 0.062437412247740756 Iteration 7: loglikelihood = -1381.0278498078874, backtracks = 0, tol = 0.07731360202039332 Iteration 8: loglikelihood = -1377.9712209079762, backtracks = 0, tol = 0.08607302665784919 Iteration 9: loglikelihood = -1369.8593010160466, backtracks = 0, tol = 0.08567504754601805 Iteration 10: loglikelihood = -1368.0189323176792, backtracks = 0, tol = 0.07838976570521924 Iteration 11: loglikelihood = -1362.7972183832405, backtracks = 0, tol = 0.07817420154884056 Iteration 12: loglikelihood = -1359.6609749335778, backtracks = 0, tol = 0.007597582290976929 Iteration 13: loglikelihood = -1357.28409515, backtracks = 0, tol = 0.001402603588014077 Iteration 14: loglikelihood = -1355.2169442890386, backtracks = 0, tol = 0.0005268128104243887 Iteration 15: loglikelihood = -1353.4286048129848, backtracks = 0, tol = 0.00033966288163165095 Iteration 16: loglikelihood = -1351.8563843154268, backtracks = 0, tol = 0.00032352392126996064 Iteration 17: loglikelihood = -1349.3917111244236, backtracks = 1, tol = 0.00018692149121900245 Iteration 18: loglikelihood = -1347.5452038845776, backtracks = 1, tol = 0.0003660307923422943 Iteration 19: loglikelihood = -1346.0561619362281, backtracks = 1, tol = 0.0004141128432150306 Iteration 20: loglikelihood = -1344.8395565748513, backtracks = 1, tol = 0.00041081657747346156 Iteration 21: loglikelihood = -1343.8334655354386, backtracks = 1, tol = 0.0003847298581434691 Iteration 22: loglikelihood = -1342.9923881242946, backtracks = 1, tol = 0.0003506092687096066 Iteration 23: loglikelihood = -1342.2823217215173, backtracks = 1, tol = 0.00031551659761300027 Iteration 24: loglikelihood = -1341.6774657636724, backtracks = 1, tol = 0.00028256026662317303 Iteration 25: loglikelihood = -1341.1579868767537, backtracks = 1, tol = 0.00025289009462990534 Iteration 26: loglikelihood = -1340.7084673222992, backtracks = 1, tol = 0.00022672376345946198 Iteration 27: loglikelihood = -1340.316802601215, backtracks = 1, tol = 0.00020386432560647147 Iteration 28: loglikelihood = -1339.973402280364, backtracks = 1, tol = 0.0001839558224483325 Iteration 29: loglikelihood = -1339.6706012079635, backtracks = 1, tol = 0.00016660585630932432 Iteration 30: loglikelihood = -1339.4022203869874, backtracks = 1, tol = 0.0001514411856622917 Iteration 31: loglikelihood = -1339.1632364849952, backtracks = 1, tol = 0.00013812994022897464 Iteration 32: loglikelihood = -1338.9495313855361, backtracks = 1, tol = 0.00012638751403756815 Iteration 33: loglikelihood = -1338.757701308073, backtracks = 1, tol = 0.00011597481899054897 Iteration 34: loglikelihood = -1338.5849105465509, backtracks = 1, tol = 0.00010669332355825391 Iteration 35: loglikelihood = -1338.4287787712015, backtracks = 1, tol = 9.837911110527716e-5 0.370401 seconds (1.59 M allocations: 29.606 MiB) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3522.8977, backtracks = 0, tol = 0.09440768157956209 Iteration 2: loglikelihood = -3478.896, backtracks = 0, tol = 0.04460327488245252 Iteration 3: loglikelihood = -3452.2986, backtracks = 1, tol = 0.05892410048526403 Iteration 4: loglikelihood = -3446.3977, backtracks = 1, tol = 0.013377851894210572 Iteration 5: loglikelihood = -3428.952, backtracks = 1, tol = 0.06750818755752051 Iteration 6: loglikelihood = -3426.6216, backtracks = 1, tol = 0.007289504326263784 Iteration 7: loglikelihood = -3425.709, backtracks = 1, tol = 0.004482573868183805 Iteration 8: loglikelihood = -3425.4307, backtracks = 1, tol = 0.003332362040031638 Iteration 9: loglikelihood = -3425.3562, backtracks = 1, tol = 0.0018561887515357606 Iteration 10: loglikelihood = -3425.3352, backtracks = 1, tol = 0.001050634516744874 Iteration 11: loglikelihood = -3425.334, backtracks = 1, tol = 0.0005251105874020645 Iteration 12: loglikelihood = -3425.3337, backtracks = 1, tol = 0.0002749047328019482 Iteration 13: loglikelihood = -3425.3337, backtracks = 1, tol = 0.00013418806141207804 Iteration 14: loglikelihood = -3425.3335, backtracks = 1, tol = 6.909040725287948e-5 27.332312 seconds (14.63 M allocations: 661.620 MiB, 2.35% gc time, 96.29% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse NegativeBinomial regression Number of threads = 1 Link functin = LogLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -3422.6147, backtracks = 0, tol = 0.09440768157956209 Iteration 2: loglikelihood = -3313.1987, backtracks = 0, tol = 0.04588842755248953 Iteration 3: loglikelihood = -3101.926, backtracks = 1, tol = 0.05717735180163465 Iteration 4: loglikelihood = -2887.154, backtracks = 1, tol = 0.012358790384135043 Iteration 5: loglikelihood = -2665.2808, backtracks = 1, tol = 0.0077565402751612195 Iteration 6: loglikelihood = -2595.8945, backtracks = 0, tol = 0.10080336334061503 Iteration 7: loglikelihood = -2465.8037, backtracks = 0, tol = 0.11225815481928349 Iteration 8: loglikelihood = -2378.7815, backtracks = 0, tol = 0.11202251042878916 Iteration 9: loglikelihood = -2305.0437, backtracks = 0, tol = 0.1154706514378875 Iteration 10: loglikelihood = -2247.5325, backtracks = 0, tol = 0.11406194299067074 Iteration 11: loglikelihood = -2210.2458, backtracks = 0, tol = 0.11728564905991788 Iteration 12: loglikelihood = -2181.085, backtracks = 0, tol = 0.11580435946379247 Iteration 13: loglikelihood = -2167.7458, backtracks = 0, tol = 0.11798274640349211 Iteration 14: loglikelihood = -2154.9824, backtracks = 0, tol = 0.11664548414487737 Iteration 15: loglikelihood = -2152.8867, backtracks = 0, tol = 0.11842338592490062 Iteration 16: loglikelihood = -2146.7039, backtracks = 0, tol = 0.11719872832388058 Iteration 17: loglikelihood = -2140.7424, backtracks = 1, tol = 0.020296833887863984 Iteration 18: loglikelihood = -2139.7947, backtracks = 1, tol = 0.007748464077982127 Iteration 19: loglikelihood = -2139.6409, backtracks = 0, tol = 0.10586609856964613 Iteration 20: loglikelihood = -2137.4023, backtracks = 0, tol = 0.10574401759457629 Iteration 21: loglikelihood = -2135.9702, backtracks = 1, tol = 0.013833712362984883 Iteration 22: loglikelihood = -2135.6978, backtracks = 1, tol = 0.005675410275931488 Iteration 23: loglikelihood = -2135.6333, backtracks = 1, tol = 0.002536959633693427 Iteration 24: loglikelihood = -2135.6123, backtracks = 1, tol = 0.0015117348560636516 Iteration 25: loglikelihood = -2135.6038, backtracks = 1, tol = 0.00087289356351016 Iteration 26: loglikelihood = -2135.6023, backtracks = 1, tol = 0.0004975636367927709 Iteration 27: loglikelihood = -2135.5996, backtracks = 1, tol = 0.0002829413255173056 Iteration 28: loglikelihood = -2135.601, backtracks = 3, tol = 4.023966070034946e-5 0.232730 seconds (1.62 M allocations: 26.970 MiB, 7.32% gc time) Test Summary: | Pass Total Time Negative binomial nuisance parameter Float32 matrix | 12 12 31.9s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, dt::Int64, desc::String, barlen::Nothing, color::Symbol, output::Base.PipeEndpoint; offset::Int64) at deprecated.jl:1 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:1 Running sparse linear regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 10 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2896.6116813943763, backtracks = 0, tol = 1.0257704354307222 Iteration 2: loglikelihood = -1753.4720992614753, backtracks = 0, tol = 0.28706825512903816 Iteration 3: loglikelihood = -1460.3823326395225, backtracks = 0, tol = 0.1059822007319242 Iteration 4: loglikelihood = -1438.5292259047123, backtracks = 0, tol = 0.028655431669451118 Iteration 5: loglikelihood = -1438.0856032112097, backtracks = 0, tol = 0.0034955373515602557 Iteration 6: loglikelihood = -1438.0744350329464, backtracks = 0, tol = 0.0005882060650840543 Iteration 7: loglikelihood = -1438.0741395461057, backtracks = 0, tol = 8.427264473927088e-5 5.012402 seconds (1.02 M allocations: 132.819 MiB, 1.33% gc time, 90.39% compilation time) Test Summary: | Pass Total Time initialze beta | 1 1 5.4s 10.156601 seconds (4.00 M allocations: 82.389 MiB, 0.31% gc time, 0.68% compilation time) 5.324630 seconds (3.98 M allocations: 91.678 MiB, 0.43% gc time) 10.755116 seconds (20.38 M allocations: 438.638 MiB, 0.77% gc time, 17.26% compilation time: 78% of which was recompilation) 8.586564 seconds (20.18 M allocations: 434.190 MiB, 0.95% gc time) 38.027095 seconds (3.36 M allocations: 4.228 GiB, 6.63% gc time, 30.48% compilation time) 54.529058 seconds (72.50 k allocations: 183.670 MiB, 0.28% gc time) Test Summary: | Pass Total Time memory_efficient keyword | 7 7 2m26.6s Test Summary: | Pass Total Time update_support! | 10 10 0.6s 15.245 ms (78 allocations: 4.56 KiB) 4.326 μs (0 allocations: 0 bytes) 143.359 μs (4 allocations: 288 bytes) 6.935 μs (0 allocations: 0 bytes) 48.429 μs (2 allocations: 64 bytes) 31.259 μs (0 allocations: 0 bytes) 32.990 μs (0 allocations: 0 bytes) 31.770 μs (0 allocations: 0 bytes) 106.589 μs (0 allocations: 0 bytes) 39.578 ms (78 allocations: 4.56 KiB) 18.320 μs (0 allocations: 0 bytes) 175.179 μs (4 allocations: 288 bytes) 34.980 μs (0 allocations: 0 bytes) 238.638 μs (2 allocations: 64 bytes) 89.119 μs (0 allocations: 0 bytes) 174.409 μs (0 allocations: 0 bytes) 168.878 μs (0 allocations: 0 bytes) 211.698 μs (0 allocations: 0 bytes) Test Summary: | Total Time benchmarks for multivariate function | 0 2m11.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2900.9186300194497, backtracks = 0, tol = 0.1480224208200413 Iteration 2: loglikelihood = -2869.406464695619, backtracks = 0, tol = 0.035126790460779864 Iteration 3: loglikelihood = -2868.084702693443, backtracks = 0, tol = 0.0055693496163324524 Iteration 4: loglikelihood = -2868.034423817725, backtracks = 0, tol = 0.001118951762895177 Iteration 5: loglikelihood = -2868.030857635375, backtracks = 0, tol = 0.00031182601179138955 Iteration 6: loglikelihood = -2868.0305288614227, backtracks = 0, tol = 0.00010393305949947338 Iteration 7: loglikelihood = -2868.0304966516946, backtracks = 0, tol = 3.100862049859014e-5 0.457292 seconds (43.84 k allocations: 5.329 MiB, 65.10% compilation time) Test Summary: | Pass Total Time multivariate fit_iht SnpLinAlg | 7 7 13.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Running sparse Multivariate Gaussian regression Number of threads = 1 Link functin = IdentityLink() Sparsity parameter (k) = 12 Prior weight scaling = off Doubly sparse projection = off Debias = off Max IHT iterations = 200 Converging when tol < 0.0001 and iteration ≥ 5: Iteration 1: loglikelihood = -2878.028812628852, backtracks = 0, tol = 2.5661768673084553 Iteration 2: loglikelihood = -2868.563037890196, backtracks = 0, tol = 0.024335274263285057 Iteration 3: loglikelihood = -2868.0815051475474, backtracks = 0, tol = 0.004072558228741048 Iteration 4: loglikelihood = -2868.0352100240902, backtracks = 0, tol = 0.0013135682973484317 Iteration 5: loglikelihood = -2868.0309297231934, backtracks = 0, tol = 0.000386434110747091 Iteration 6: loglikelihood = -2868.0305335492912, backtracks = 0, tol = 0.00011924564415557833 Iteration 7: loglikelihood = -2868.0304968517494, backtracks = 0, tol = 3.603726989721193e-5 2.017664 seconds (256.78 k allocations: 167.471 MiB, 56.74% compilation time) Test Summary: | Pass Total Time initialze beta | 5 5 2.6s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** ┌ Warning: accessing `Type.name` is deprecated without replacement. If for detection, use `Base.isType(x)`. │ caller = ProgressMeter.Progress(n::Int64, desc::String, offset::Int64; kwargs::Base.Pairs{Symbol, Union{}, Nothing, @NamedTuple{}}) at deprecated.jl:5 └ @ ProgressMeter ~/.julia/packages/ProgressMeter/N660J/src/deprecated.jl:5 Cross validating... 3%|█ | ETA: 0:03:56 Cross validating... 11%|███▌ | ETA: 0:01:06 Cross validating... 14%|████▋ | ETA: 0:00:50 Cross validating... 17%|█████▋ | ETA: 0:00:40 Cross validating... 21%|██████▋ | ETA: 0:00:33 Cross validating... 24%|███████▋ | ETA: 0:00:28 Cross validating... 27%|████████▋ | ETA: 0:00:24 Cross validating... 30%|█████████▋ | ETA: 0:00:21 Cross validating... 33%|██████████▋ | ETA: 0:00:19 Cross validating... 37%|███████████▋ | ETA: 0:00:17 Cross validating... 40%|████████████▊ | ETA: 0:00:15 Cross validating... 43%|█████████████▊ | ETA: 0:00:13 Cross validating... 46%|██████████████▊ | ETA: 0:00:12 Cross validating... 49%|███████████████▊ | ETA: 0:00:11 Cross validating... 52%|████████████████▊ 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validating... 100%|████████████████████████████████| Time: 0:00:12 Crossvalidation Results: k MSE 0 4850.349883646026 1 3511.4081163548626 2 2186.2436867560555 3 1657.3383534153786 4 1262.9499312618798 5 844.929522459847 6 479.60221365642934 7 422.85416626905 8 326.2992304148046 9 329.1772584647673 10 333.0631966707711 11 336.0692807952061 12 337.1648792324418 13 340.01524706994337 14 341.52212507177023 15 344.8836044782023 16 362.06791814028657 17 377.519558366468 18 346.79039323123015 19 347.0962998229421 20 375.26500662652177 Best k = 8 12.883124 seconds (11.77 M allocations: 312.964 MiB, 1.76% gc time, 61.69% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:04 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 62%|███████████████████▊ | ETA: 0:00:02 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 4850.349883646026 1 3513.0133680708004 2 2194.7902872144714 3 1660.0100180573352 4 1269.2132728028328 5 850.0220553226893 6 486.8280061453004 7 431.4510313811508 8 335.76800661293487 9 343.83501871770585 10 353.7850291766922 11 362.56185427768423 12 371.1667833246926 13 380.18858431866516 14 380.39587589722817 15 387.60892229205234 16 385.15315216657547 17 392.7266014255879 18 400.265330711409 19 396.25744235489503 20 399.0959993617999 Best k = 8 5.128811 seconds (10.86 M allocations: 229.762 MiB, 0.91% gc time, 1.05% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, normal model | 3 3 18.8s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:06:22 Cross validating... 8%|██▌ | ETA: 0:02:26 Cross validating... 13%|████▏ | ETA: 0:01:28 Cross validating... 17%|█████▋ | ETA: 0:01:01 Cross validating... 22%|███████▏ | ETA: 0:00:46 Cross validating... 27%|████████▋ | ETA: 0:00:36 Cross validating... 32%|██████████▏ | ETA: 0:00:29 Cross validating... 37%|███████████▋ | ETA: 0:00:23 Cross validating... 43%|█████████████▊ | ETA: 0:00:18 Cross validating... 49%|███████████████▊ | ETA: 0:00:14 Cross validating... 54%|█████████████████▎ | ETA: 0:00:12 Cross validating... 59%|██████████████████▊ | ETA: 0:00:10 Cross validating... 63%|████████████████████▍ | ETA: 0:00:08 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:07 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:05 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:04 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:02 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:02 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:15 Crossvalidation Results: k MSE 0 1607.249146484375 1 1279.3864790039063 2 977.5503674316406 3 796.0235600585938 4 640.0029982910157 5 536.1754584960938 6 447.5910556640624 7 393.0231287841797 8 361.9664696044922 9 355.8810760498047 10 360.1738742675781 11 360.3294991455078 12 352.3402239990234 13 355.17762878417966 14 365.2615573730469 15 382.52893005371095 16 363.7806417236328 17 363.6109025878906 18 366.5676458740234 19 375.68886206054685 20 381.0694328613281 Best k = 12 16.310945 seconds (12.54 M allocations: 311.689 MiB, 0.65% gc time, 84.05% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 6%|██ | ETA: 0:00:02 Cross validating... 13%|████▏ | ETA: 0:00:02 Cross validating... 17%|█████▋ | ETA: 0:00:02 Cross validating... 22%|███████▏ | ETA: 0:00:02 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 30%|█████████▋ | ETA: 0:00:02 Cross validating... 35%|███████████▏ | ETA: 0:00:02 Cross validating... 41%|█████████████▎ | ETA: 0:00:01 Cross validating... 48%|███████████████▎ | ETA: 0:00:01 Cross validating... 52%|████████████████▊ | ETA: 0:00:01 Cross validating... 57%|██████████████████▎ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:00 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:02 Crossvalidation Results: k MSE 0 1607.249146484375 1 1281.053293457031 2 979.0096721191408 3 797.9697836914063 4 641.5501442871093 5 544.4125745849609 6 457.5381704101562 7 396.54611840820314 8 362.3918896484375 9 367.96467565917965 10 377.42023278808597 11 378.0402138671875 12 370.8656447753906 13 381.4650789794922 14 395.73029235839846 15 400.58226586914066 16 402.2412879638672 17 405.38371984863284 18 406.67606823730466 19 415.63111901855467 20 421.15609521484373 Best k = 8 2.647827 seconds (10.81 M allocations: 198.153 MiB, 1.76% gc time, 1.70% compilation time) Test Summary: | Pass Total Time Cross validation on Float32 matrix, normal model | 2 2 20.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:01 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 8%|██▌ | ETA: 0:00:26 Cross validating... 11%|███▌ | ETA: 0:00:19 Cross validating... 14%|████▋ | ETA: 0:00:16 Cross validating... 17%|█████▋ | ETA: 0:00:13 Cross 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validating... 76%|████████████████████████▍ | ETA: 0:00:02 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:02 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:01 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 463.62761849179924 1 392.1981841278806 2 328.73010243093466 3 298.7740300433594 4 258.50686435208786 5 233.0255203088922 6 202.0730084094006 7 201.75547578574117 8 200.32669193323318 9 203.41364114547346 10 197.45532354649345 11 209.20027728793536 12 210.87523094779047 13 219.09839847885002 14 206.46923275995306 15 219.90894493652604 16 240.71094401830385 17 237.50152861616644 18 223.95086235361288 19 245.63225580532418 20 236.06313607945367 Best k = 10 8.159501 seconds (16.56 M allocations: 381.905 MiB, 0.94% gc time, 32.18% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:04 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 30%|█████████▋ | ETA: 0:00:04 Cross validating... 33%|██████████▋ | ETA: 0:00:04 Cross validating... 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Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 463.62761849179924 1 392.6356369845147 2 329.0772149480608 3 299.46808525865293 4 259.90566623335104 5 234.83373628736365 6 204.64326196786158 7 206.54228017689286 8 205.49271344207256 9 206.5230625193368 10 207.98821389255681 11 218.75032679479187 12 228.9021915333765 13 225.01968012034985 14 226.85553654383847 15 249.0543574294074 16 253.4609738052692 17 243.3677728436497 18 260.82313506069625 19 255.9446624241296 20 238.57041988762015 Best k = 6 5.735527 seconds (17.67 M allocations: 365.963 MiB, 1.05% gc time, 1.07% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, logistic model | 2 2 14.4s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:44 Cross validating... 8%|██▌ | ETA: 0:00:18 Cross validating... 11%|███▌ | ETA: 0:00:14 Cross validating... 14%|████▋ | ETA: 0:00:11 Cross validating... 17%|█████▋ | ETA: 0:00:10 Cross validating... 21%|██████▋ | ETA: 0:00:08 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:06 Cross validating... 35%|███████████▏ | ETA: 0:00:05 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:04 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:03 Cross validating... 59%|██████████████████▊ | ETA: 0:00:03 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:02 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:02 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 461.3869152770952 1 431.55705817834604 2 389.958449446312 3 379.72106717974236 4 370.3664245658389 5 355.27431890602986 6 335.7111176184301 7 336.4924106054001 8 323.54441244584945 9 324.6935651314436 10 328.06629532266413 11 332.46509606183514 12 332.67831806230885 13 335.66441991613885 14 338.7693003233039 15 344.19426986867927 16 369.51492231744817 17 388.624010660123 18 347.84253730069383 19 368.7761550313349 20 372.2155632160352 Best k = 8 7.007180 seconds (16.52 M allocations: 394.630 MiB, 7.17% gc time, 34.81% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:03 Cross validating... 6%|██ | ETA: 0:00:03 Cross validating... 10%|███ | ETA: 0:00:03 Cross validating... 13%|████▏ | ETA: 0:00:03 Cross validating... 16%|█████▏ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:03 Cross validating... 29%|█████████▏ | ETA: 0:00:03 Cross validating... 32%|██████████▏ | ETA: 0:00:03 Cross validating... 35%|███████████▏ | ETA: 0:00:03 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:02 Cross validating... 44%|██████████████▎ | ETA: 0:00:02 Cross validating... 48%|███████████████▎ | ETA: 0:00:02 Cross validating... 51%|████████████████▎ | ETA: 0:00:02 Cross validating... 54%|█████████████████▎ | ETA: 0:00:02 Cross validating... 57%|██████████████████▎ | ETA: 0:00:02 Cross validating... 60%|███████████████████▎ | ETA: 0:00:02 Cross validating... 63%|████████████████████▍ | ETA: 0:00:02 Cross validating... 67%|█████████████████████▍ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 76%|████████████████████████▍ | ETA: 0:00:01 Cross validating... 79%|█████████████████████████▍ | ETA: 0:00:01 Cross validating... 83%|██████████████████████████▍ | ETA: 0:00:01 Cross validating... 86%|███████████████████████████▍ | ETA: 0:00:01 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:00 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:00 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:04 Crossvalidation Results: k MSE 0 461.3869152770952 1 432.05897355602167 2 390.934211770521 3 381.37901476982836 4 368.7071934252741 5 358.20443388884854 6 339.1177147889047 7 344.26432259849025 8 332.66619963212975 9 336.78029791777266 10 343.2244743711477 11 357.48239433981985 12 363.50541012399617 13 357.6327190554543 14 379.70616544500547 15 391.17300819403647 16 403.7733810140973 17 409.7133350232342 18 405.1569725321302 19 404.0743082034487 20 412.60798603154535 Best k = 8 4.336386 seconds (17.42 M allocations: 358.321 MiB, 1.26% gc time, 1.04% compilation time) Test Summary: | Pass Total Time Cross validation on Float64 matrix, logistic model | 2 2 12.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:00 Cross validating... 6%|██ | ETA: 0:00:32 Cross validating... 10%|███ | ETA: 0:00:22 Cross validating... 13%|████▏ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:11 Cross validating... 24%|███████▋ | ETA: 0:00:10 Cross validating... 27%|████████▋ | ETA: 0:00:09 Cross validating... 30%|█████████▋ | ETA: 0:00:08 Cross validating... 33%|██████████▋ | ETA: 0:00:08 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 40%|████████████▊ | ETA: 0:00:06 Cross validating... 43%|█████████████▊ | ETA: 0:00:06 Cross validating... 46%|██████████████▊ | ETA: 0:00:05 Cross validating... 49%|███████████████▊ | ETA: 0:00:05 Cross validating... 52%|████████████████▊ | ETA: 0:00:04 Cross validating... 56%|█████████████████▊ | ETA: 0:00:04 Cross validating... 59%|██████████████████▊ | ETA: 0:00:04 Cross validating... 62%|███████████████████▊ | ETA: 0:00:03 Cross validating... 65%|████████████████████▉ | ETA: 0:00:03 Cross validating... 68%|█████████████████████▉ | ETA: 0:00:03 Cross validating... 71%|██████████████████████▉ | ETA: 0:00:02 Cross validating... 75%|███████████████████████▉ | ETA: 0:00:02 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:02 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:02 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:01 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:01 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:07 Crossvalidation Results: k MSE 0 1064.779257486441 1 921.6462143008596 2 716.3445526342832 3 580.8003951381215 4 495.043900874571 5 440.4645138705616 6 385.4813605775712 7 383.3735176314855 8 397.3778629584514 9 396.7393827406207 10 391.37549364083463 11 396.26850082825615 12 398.86124991129384 13 402.39190361253196 14 402.45434726217275 15 393.2673869202781 16 403.9231386739334 17 437.97410110962574 18 421.4375065810664 19 418.9811900872181 20 441.3860680116088 Best k = 7 8.359122 seconds (15.75 M allocations: 367.033 MiB, 1.01% gc time, 31.11% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:04 Cross validating... 6%|██ | ETA: 0:00:05 Cross validating... 10%|███ | ETA: 0:00:05 Cross validating... 13%|████▏ | ETA: 0:00:05 Cross validating... 16%|█████▏ | ETA: 0:00:05 Cross validating... 19%|██████▏ | ETA: 0:00:04 Cross validating... 22%|███████▏ | ETA: 0:00:04 Cross validating... 25%|████████▏ | ETA: 0:00:04 Cross validating... 29%|█████████▏ | ETA: 0:00:04 Cross validating... 32%|██████████▏ | ETA: 0:00:04 Cross validating... 35%|███████████▏ | ETA: 0:00:04 Cross validating... 38%|████████████▎ | ETA: 0:00:03 Cross validating... 41%|█████████████▎ | ETA: 0:00:03 Cross validating... 44%|██████████████▎ | ETA: 0:00:03 Cross validating... 48%|███████████████▎ | ETA: 0:00:03 Cross validating... 51%|████████████████▎ | 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validating... 100%|████████████████████████████████| Time: 0:00:05 Crossvalidation Results: k MSE 0 1064.779257486441 1 878.0314218677762 2 691.0696546963914 3 575.369475848875 4 489.75963460026225 5 437.94851786874256 6 382.61259206614295 7 393.51840326481715 8 398.16968511520304 9 403.9632691612888 10 403.8272009584546 11 409.4526673500279 12 414.863146239609 13 430.4678052743775 14 423.1481464033376 15 421.53655977712714 16 436.31383317126097 17 451.31796799997363 18 443.8634294905776 19 452.1793484066307 20 462.5694170528151 Best k = 6 5.605109 seconds (14.74 M allocations: 300.014 MiB, 1.05% gc time, 1.08% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, Poisson model | 2 2 14.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 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validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:01 Cross validating... 100%|████████████████████████████████| Time: 0:00:44 Crossvalidation Results: k MSE 0 410.50588295179904 1 347.2011497351312 2 289.00537764335087 3 266.3668125019432 4 245.49117991055215 5 222.32069189514715 6 204.21870021295422 7 202.54700584908838 8 204.59811338740275 9 205.48732671237508 10 207.94216799739849 11 207.8884558058784 12 210.26218701041157 13 211.09998764866856 14 212.29991243254534 15 213.55812694191573 16 214.6542958810353 17 213.96247209926963 18 214.21769946356227 19 215.48385603108997 20 215.90123444311166 Best k = 7 44.845268 seconds (136.24 M allocations: 3.394 GiB, 1.20% gc time, 5.01% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:00:07 Cross validating... 5%|█▌ | ETA: 0:00:07 Cross validating... 6%|██ | ETA: 0:00:07 Cross validating... 8%|██▌ | ETA: 0:00:07 Cross validating... 10%|███ | ETA: 0:00:06 Cross validating... 13%|████▏ | ETA: 0:00:06 Cross validating... 14%|████▋ | ETA: 0:00:06 Cross validating... 16%|█████▏ | ETA: 0:00:06 Cross validating... 17%|█████▋ | ETA: 0:00:06 Cross validating... 19%|██████▏ | ETA: 0:00:07 Cross validating... 21%|██████▋ | ETA: 0:00:07 Cross validating... 22%|███████▏ | ETA: 0:00:07 Cross validating... 24%|███████▋ | ETA: 0:00:07 Cross validating... 25%|████████▏ | ETA: 0:00:07 Cross validating... 27%|████████▋ | ETA: 0:00:07 Cross validating... 29%|█████████▏ | ETA: 0:00:07 Cross validating... 30%|█████████▋ | ETA: 0:00:07 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 33%|██████████▋ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:07 Cross validating... 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0:00:01 Cross validating... 95%|██████████████████████████████▌ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 98%|███████████████████████████████▌| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:11 Crossvalidation Results: k MSE 0 410.50588295179904 1 346.1453702598687 2 290.180703968784 3 269.52700433400025 4 248.8358317635645 5 225.34493468696348 6 207.11503584789466 7 205.73978626704024 8 209.8326606693813 9 214.0059842223733 10 217.04006459012672 11 223.08709126516663 12 226.32017612354562 13 230.37872913202688 14 235.14449886533913 15 242.8612264045338 16 243.1935842825999 17 246.8858033900537 18 253.63266314048127 19 259.18205259561404 20 262.4268354860662 Best k = 7 11.779950 seconds (34.42 M allocations: 710.847 MiB, 1.41% gc time, 0.65% compilation time) Test Summary: | Pass Total Time Cross validation on SnpLinAlg, NegativeBinomial model | 2 2 57.1s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 3%|█ | ETA: 0:01:08 Cross validating... 6%|██ | ETA: 0:00:34 Cross validating... 10%|███ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:18 Cross validating... 16%|█████▏ | ETA: 0:00:14 Cross validating... 19%|██████▏ | ETA: 0:00:12 Cross validating... 22%|███████▏ | ETA: 0:00:10 Cross validating... 25%|████████▏ | ETA: 0:00:09 Cross validating... 29%|█████████▏ | ETA: 0:00:08 Cross validating... 32%|██████████▏ | ETA: 0:00:07 Cross validating... 37%|███████████▋ | ETA: 0:00:06 Cross validating... 40%|████████████▊ | ETA: 0:00:05 Cross validating... 43%|█████████████▊ | ETA: 0:00:05 Cross validating... 46%|██████████████▊ | ETA: 0:00:04 Cross validating... 49%|███████████████▊ | ETA: 0:00:04 Cross validating... 52%|████████████████▊ | 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Crossvalidation Results: k MSE 0 708.7406597900391 1 594.0547950439453 2 472.60887115478516 3 391.07051165771486 4 322.2429605712891 5 274.1304553527832 6 242.98796069335935 7 231.75397763061522 8 211.04413333129884 9 208.82878451538085 10 210.9139321594238 11 206.8662128601074 12 209.29315435791017 13 216.44690969848637 14 210.83974066162108 15 223.69269552612303 16 223.5122525024414 17 217.3672544555664 18 230.29235778808595 19 245.48900619506838 20 214.24631561279296 Best k = 11 6.284919 seconds (17.19 M allocations: 341.593 MiB, 1.63% gc time, 45.07% compilation time) **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 5%|█▌ | ETA: 0:00:03 Cross validating... 8%|██▌ | ETA: 0:00:03 Cross validating... 11%|███▌ | ETA: 0:00:03 Cross validating... 14%|████▋ | ETA: 0:00:03 Cross validating... 19%|██████▏ | ETA: 0:00:03 Cross validating... 22%|███████▏ | ETA: 0:00:03 Cross validating... 25%|████████▏ | ETA: 0:00:02 Cross validating... 29%|█████████▏ | ETA: 0:00:02 Cross validating... 32%|██████████▏ | ETA: 0:00:02 Cross validating... 37%|███████████▋ | ETA: 0:00:02 Cross validating... 40%|████████████▊ | ETA: 0:00:02 Cross validating... 43%|█████████████▊ | ETA: 0:00:02 Cross validating... 46%|██████████████▊ | ETA: 0:00:02 Cross validating... 49%|███████████████▊ | ETA: 0:00:02 Cross validating... 52%|████████████████▊ | ETA: 0:00:02 Cross validating... 56%|█████████████████▊ | ETA: 0:00:01 Cross validating... 59%|██████████████████▊ | ETA: 0:00:01 Cross validating... 62%|███████████████████▊ | ETA: 0:00:01 Cross validating... 65%|████████████████████▉ | ETA: 0:00:01 Cross validating... 70%|██████████████████████▍ | ETA: 0:00:01 Cross validating... 73%|███████████████████████▍ | ETA: 0:00:01 Cross validating... 78%|████████████████████████▉ | ETA: 0:00:01 Cross validating... 81%|█████████████████████████▉ | ETA: 0:00:01 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:01 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:00 Cross validating... 90%|█████████████████████████████ | ETA: 0:00:00 Cross validating... 94%|██████████████████████████████ | ETA: 0:00:00 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:03 Crossvalidation Results: k MSE 0 708.7406597900391 1 575.6241903076173 2 458.4867525024414 3 380.67050573730467 4 317.43561486816407 5 274.8225385131836 6 243.94065100097657 7 233.23877688598634 8 212.74209445190428 9 214.86823376464844 10 213.80905279541014 11 216.52949041748047 12 220.7860779724121 13 222.78791012573242 14 231.40656030273436 15 233.06280703735348 16 243.6403890075684 17 242.80908297729493 18 238.556499420166 19 251.23290313720705 20 244.79654568481442 Best k = 8 3.450292 seconds (16.26 M allocations: 288.182 MiB, 1.85% gc time, 1.86% compilation time) Test Summary: | Pass Total Time Cross validation on floating point matrices, NegativeBinomial model | 2 2 10.3s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:01:22 Cross validating... 3%|█ | ETA: 0:00:57 Cross validating... 4%|█▎ | ETA: 0:00:45 Cross validating... 5%|█▋ | ETA: 0:00:38 Cross validating... 6%|█▉ | ETA: 0:00:33 Cross validating... 7%|██▎ | ETA: 0:00:30 Cross validating... 8%|██▌ | ETA: 0:00:28 Cross validating... 9%|██▉ | ETA: 0:00:26 Cross validating... 10%|███▎ | ETA: 0:00:25 Cross validating... 11%|███▌ | ETA: 0:00:24 Cross validating... 12%|███▉ | ETA: 0:00:23 Cross validating... 13%|████▏ | ETA: 0:00:23 Cross validating... 14%|████▌ | ETA: 0:00:22 Cross 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100%|████████████████████████████████| Time: 0:00:17 Crossvalidation Results: k MSE 1 4341.6844396767765 2 3901.3792877705173 3 3610.059806470797 4 3420.584737825683 5 3369.0098490037335 6 3331.250074068859 7 3312.5012894478414 8 3344.2221615058015 9 3396.3089804646634 10 3448.3580271543333 11 3438.2388442995098 12 3459.7616658978804 13 3503.216256993699 14 3525.634404831802 15 3563.5889551982073 16 3607.2894931586543 17 3644.0943184366606 18 3689.3661672479666 19 3722.111412983519 20 3732.4486308776955 Best k = 7 17.982778 seconds (308.52 k allocations: 212.314 MiB, 0.56% gc time, 9.52% compilation time) Test Summary: | Pass Total Time multivariate cross validation SnpLinAlg | 3 3 22.8s Test Summary: | Pass Total Time wrapper univariate | 20 20 2m05.2s **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:15 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:19 Cross validating... 18%|█████▊ | ETA: 0:00:18 Cross validating... 19%|██████▏ | ETA: 0:00:19 Cross validating... 20%|██████▍ | ETA: 0:00:19 Cross validating... 21%|██████▊ | ETA: 0:00:18 Cross validating... 22%|███████ | ETA: 0:00:18 Cross validating... 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0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:10 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ | ETA: 0:00:14 Cross validating... 11%|███▌ | ETA: 0:00:15 Cross validating... 12%|███▉ | ETA: 0:00:16 Cross validating... 13%|████▏ | ETA: 0:00:16 Cross validating... 14%|████▌ | ETA: 0:00:17 Cross validating... 15%|████▊ | ETA: 0:00:17 Cross validating... 16%|█████▏ | ETA: 0:00:18 Cross validating... 17%|█████▌ | ETA: 0:00:18 Cross 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2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 **** MendelIHT Version 1.4.11 **** **** Benjamin Chu, Kevin Keys, Chris German, Hua Zhou **** **** Jin Zhou, Eric Sobel, Janet Sinsheimer, Kenneth Lange **** **** **** **** Please cite our paper! **** **** https://doi.org/10.1093/gigascience/giaa044 **** Cross validating... 2%|▋ | ETA: 0:00:11 Cross validating... 3%|█ | ETA: 0:00:10 Cross validating... 4%|█▎ | ETA: 0:00:11 Cross validating... 5%|█▋ | ETA: 0:00:11 Cross validating... 6%|█▉ | ETA: 0:00:12 Cross validating... 7%|██▎ | ETA: 0:00:13 Cross validating... 8%|██▌ | ETA: 0:00:13 Cross validating... 9%|██▉ | ETA: 0:00:14 Cross validating... 10%|███▎ 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82%|██████████████████████████▎ | ETA: 0:00:04 Cross validating... 83%|██████████████████████████▌ | ETA: 0:00:04 Cross validating... 84%|██████████████████████████▉ | ETA: 0:00:04 Cross validating... 85%|███████████████████████████▎ | ETA: 0:00:03 Cross validating... 86%|███████████████████████████▌ | ETA: 0:00:03 Cross validating... 87%|███████████████████████████▉ | ETA: 0:00:03 Cross validating... 88%|████████████████████████████▏ | ETA: 0:00:03 Cross validating... 89%|████████████████████████████▌ | ETA: 0:00:03 Cross validating... 90%|████████████████████████████▊ | ETA: 0:00:02 Cross validating... 91%|█████████████████████████████▏ | ETA: 0:00:02 Cross validating... 92%|█████████████████████████████▌ | ETA: 0:00:02 Cross validating... 93%|█████████████████████████████▊ | ETA: 0:00:02 Cross validating... 94%|██████████████████████████████▏ | ETA: 0:00:01 Cross validating... 95%|██████████████████████████████▍ | ETA: 0:00:01 Cross validating... 96%|██████████████████████████████▊ | ETA: 0:00:01 Cross validating... 97%|███████████████████████████████ | ETA: 0:00:01 Cross validating... 98%|███████████████████████████████▍| ETA: 0:00:00 Cross validating... 99%|███████████████████████████████▋| ETA: 0:00:00 Cross validating... 100%|████████████████████████████████| Time: 0:00:24 Crossvalidation Results: k MSE 1 2838.788679198002 2 2514.3973428708136 3 2305.6176519676274 4 2222.025304867614 5 2075.1670384588365 6 2067.7948989723845 7 2053.427506114907 8 2086.405384830965 9 2080.984460901671 10 2105.131199502364 11 2132.407165368786 12 2138.267187460652 13 2166.002210829576 14 2194.9918295115804 15 2189.890403738045 16 2191.181293229578 17 2209.4669750564362 18 2221.2595493644303 19 2238.7425945763257 20 2253.9559571797727 Best k = 7 Test Summary: | Pass Total Time wrapper multivariate | 8 8 1m28.1s read BGEN and VCF: Error During Test at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 Got exception outside of a @test startproc must be called before process Stacktrace: [1] error(s::String) @ Base error.jl:56 [2] process(codec::CodecZlib.ZlibDecompressor, input::TranscodingStreams.Memory, output::TranscodingStreams.Memory, error_ref::TranscodingStreams.Error) @ CodecZlib ~/.julia/packages/CodecZlib/lEc2s/src/decompression.jl:186 [3] decompress(io::IOStream, v::Variant, h::BGEN.Header; decompressed::Nothing) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:72 [4] first_allele_dosage!(b::Bgen, v::Variant; T::Type, mean_impute::Bool, clear_decompressed::Bool, data::Nothing, decompressed::Nothing, is_decompressed::Bool) @ BGEN ~/.julia/packages/BGEN/dfgRU/src/genotypes.jl:571 [5] convert_bgen_gt(t::Type{Float64}, b::Bgen) @ MendelIHT ~/.julia/packages/MendelIHT/ZcxZT/src/wrapper.jl:380 [6] macro expansion @ ./timing.jl:741 [inlined] [7] macro expansion @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:187 [inlined] [8] macro expansion @ /opt/julia/share/julia/stdlib/v1.14/Test/src/Test.jl:2246 [inlined] [9] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:185 [10] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [11] top-level scope @ ~/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 [12] include(mapexpr::Function, mod::Module, _path::String) @ Base Base.jl:326 [13] top-level scope @ none:6 [14] eval(m::Module, e::Any) @ Core boot.jl:522 [15] exec_options(opts::Base.JLOptions) @ Base client.jl:321 [16] _start() @ Base client.jl:596 Test Summary: | Error Total Time read BGEN and VCF | 1 1 2.8s RNG of the outermost testset: Xoshiro(0x7e3d2060b4762ff1, 0x4f4355fee2c5cb1b, 0xd5c1ec617cc45ec0, 0x2bb28bb79aadadfe, 0xcab2924a075d2cf4) ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken. in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/wrapper_test.jl:184 in expression starting at /home/pkgeval/.julia/packages/MendelIHT/ZcxZT/test/runtests.jl:20 Testing failed after 1111.98s ERROR: LoadError: Package MendelIHT errored during testing Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Types.jl:68 [2] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, julia_args::Cmd, test_args::Cmd, test_fn::Nothing, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.14/Pkg/src/Operations.jl:3247 [3] test(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; coverage::Bool, test_fn::Nothing, julia_args::Cmd, test_args::Cmd, force_latest_compatible_version::Bool, allow_earlier_backwards_compatible_versions::Bool, allow_reresolve::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:587 [4] test(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:172 [5] test(pkgs::Vector{String}; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:160 [6] test(pkg::String; kwargs::@Kwargs{julia_args::Cmd}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.14/Pkg/src/API.jl:159 [inlined] [7] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:223 [8] include(mod::Module, _path::String) @ Base Base.jl:325 [9] exec_options(opts::Base.JLOptions) @ Base client.jl:355 [10] _start() @ Base client.jl:596 in expression starting at /PkgEval.jl/scripts/evaluate.jl:214 PkgEval failed after 1261.65s: package tests unexpectedly errored